This report presents a concise review of the hydrogeology of the Cambrian Limestone Aquifer (CLA) in the Northern Territory (NT), and the ecological and cultural values sustained by its groundwater. It examines risks to these values associated with different approaches to the assessment of groundwater license applications in the CLA, including using the Top End and Arid Zone contingent rules, which apply in areas without a Water Allocation Plan (WAP), and other approaches proposed in draft WAPs (e.g., Georgina-Wiso). The report concludes with recommendations about appropriate methods and safeguards to protect the CLA’s groundwater and the values it sustains, in line with recommendations of the Pepper Inquiry. The major focus is the areas of the CLA where WAPs are in progress – Flora Tindall, Mataranka and Georgina Wiso. The Cambrian Limestone Aquifer (CLA) ranges from <50 m to over 400 m thick, covering much of the NT. The aquifer comprises inter-layered limestone and mudstone. Groundwater occurs largely within secondary porosity (fractures and karst features). The CLA is overlain by younger Cretaceous rocks; where these are absent, recharge to the aquifer and/or discharge to surface water occur. Below the CLA sits the Beetaloo sub-basin, a sequence of Proterozoic sedimentary rocks that host saline groundwater, oil and gas. The CLA occurs in three basins - Daly, Wiso, and Georgina. There is cross-basin connectivity between the equivalent limestone units within these. Local recharge within each CLA basin appears to exceed rates of throughflow between adjacent basins, based on environmental tracer data and modelling. Throughflow remains poorly quantified but appears nonetheless to be a significant part of the water balance. There are also indications of vertical inter-aquifer connectivity - e.g., deep groundwater below the CLA contributing to spring flows at Mataranka Thermal Pools (in addition to CLA groundwater). Recharge to the CLA occurs by diffuse percolation of rainfall in areas where Cretaceous cover is thin or absent, at rates generally between <1 and 30 mm/yr, increasing from south to north. There is also evidence of recharge at higher rates (>100 mm/yr), associated with karst features (e.g., sinkholes). Discharge of groundwater to the surface appears to be limited to small but environmentally and culturally significant areas, where it sustains vitally important groundwater dependent ecosystems (GDEs). Groundwater from the Tindall Limestone flows to the surface via springs, wetlands, and the channels of the Roper and Flora rivers and associated tributaries. These groundwater flows support significant vegetation communities and aquatic ecosystems within spring pools, groundwaterdependent sections of streams, and downstream waterbodies. Fauna drink from groundwater-fed pools and terrestrial vegetation utilises groundwater where the CLA water table is shallow. GDEs are also found within the aquifer matrix, i.e., stygofauna, including crustaceans, within caves and cavities in the rock. These groundwater dependent sites, waters, fauna, and vegetation and are of great cultural significance to Aboriginal peoples of the region. Aboriginal peoples’ oral accounts highlight the interconnectedness of the region’s groundwater, surface water and landscape, and both human and non-human living communities, as well as ancestral beings. WAPs are not currently in place for the region encompassing the CLA and Beetaloo sub-basin, but are expected to be finalized in 2022-23, in accordance with recommendations from the Pepper Inquiry. A draft WAP for the Georgina-Wiso region is currently open for public review. Current rules for groundwater licensing where WAPs are not finalized use the Top End and Arid Zone contingent rules, to set caps on groundwater extraction rates for consumptive use in a given area. The Top End rules allow for allocation of groundwater licenses up to a fraction (20%) of estimated recharge. This approach is broadly in line with other groundwater management jurisdictions in Australia and worldwide, which calculate a Sustainable Yield as a fraction of recharge and/or discharge with the intention of balancing extraction with a need to maintain long-term groundwater access and limit impacts on GDEs. It should be noted however, that this method and/or the value of 20% may not always achieve these aims, due to complicated re-distribution of water balances in response to groundwater extraction. It remains unclear whether extracting 20% of recharge in aquifers currently classified as Top End (such as the Tindall Limestone) would have unacceptable consequences for GDEs. Preliminary analysis indicates significantly reduced flows to the Roper River could result, which would be particularly noticeable during dry periods. The Arid Zone rules, which apply to the south of a line delineating northward and southward flowing surface water catchments of the NT, contain two clauses relevant to groundwater. The first states that licensed extractions should have no detrimental impacts on GDEs; the second allows for depletion of 80% of total pre-development groundwater storage, over a 100-year timeframe. These two aspects of the rules are contradictory. It is not possible for the first aim to be achieved if the second part is permitted. In accordance with the conclusions of the Pepper Inquiry, using storage volumes to calculate sustainable yields is not in line with ecologically sustainable development and risks harm to groundwater dependent values. Aquifers should not be described in terms of total storage when considering sustainable yields or ‘safe’ extraction rates. It is the water flows to and from the aquifer sustaining other aspects of the water cycle and dependent values (e.g., flows to springs, rivers and vegetation) that are most important in assessing sustainable yield. These flows are normally very small in comparison to the total water in an aquifer’s storage; hence, extracting even small proportions of overall storage can have significant water cycle consequences (e.g., reduced baseflows and/or loss of groundwater dependent ecosystems). The Arid Zone contingent allocation rules appear to be one of the only cases in Australia where a storage-based approach is applied to the determination of a ‘sustainable’ yield. If this approach were to be adopted in WAPs covering the CLA and Beetaloo sub-basin and/or remains in use more generally, it would allow for unsustainable development of groundwater, with serious potential consequences for groundwater dependent ecosystems, cultural values and water users. In the Daly Basin/Tindall Limestone section of the CLA, where the Mataranka springs and Roper River occur, extraction at rates that cause long-term storage depletion would endanger these and other important GDEs, by reducing spring discharge, river baseflow and water table levels. The current draft WAP for the Georgina Wiso region proposes an estimated sustainable yield (yearly extraction cap) of 262.6 GL/year, estimated to be 40% of long-term averaged recharge. It is unclear how or why the value of 40% of recharge was determined to represent a sustainable level of extraction. In the Georgina and Wiso Basins, knowledge of the water balance, hydrogeology and groundwater dependent ecosystems are currently not sufficient to fully understand the effects of such extraction. The recharge estimate used to derive the ESY is model-derived and has considerable uncertainty. It is nearly double the value derived from earlier runs of the same model, and higher than some field-based estimates, meaning the ESY may constitute a larger fraction of recharge than assumed. The current data also indicate that recharge is considerably lower than the long-term average in most years (and may be negligible under the typical climate), except for rare events where rainfall (and recharge) far exceeds the rolling long-term average. Such periods have likely occurred only three or four times over the past century. The vast majority of estimated recharge to the Georgina and Wiso basins is associated with a single event in 1974. The recurrence interval for such recharge events, and details of their mechanism remain unknown. Therefore, under the proposed ESY, in most years, significant aquifer overdraft (extraction far exceeding recharge) would be permitted. Such overdraft may occur for many consecutive years (or decades), before the next episodic recharge event occurs. Drawdown associated with consecutive years (or decades) of aquifer overdraft in the Georgina and Wiso basins would endanger stygofauna communities and reduce cross-basin discharge fluxes within the CLA, e.g., to the Tindall Limestone aquifer (upon which key GDEs noted above depend). Currently, groundwater discharge mechanism(s) from these two basins is poorly understood. There may be additional groundwater dependent ecosystems within or close to the edge of the plan area sustained by CLA groundwater (such as springs in the western Wiso Basin, or un-mapped deeprooted vegetation communities). These GDEs may suffer reduced access to groundwater for extended periods between recharge events due to extraction at the proposed ESY, threatening their survival. Water quality risks, such as migration of saline water into fresher parts of the aquifer, and potential aquifer integrity issues associated with concentrated extraction in particular regions have also received limited or no attention in the draft WAP. Better characterization of GDEs, recharge and discharge mechanisms and rates, and more comprehensive assessment of these risks are urgently required before appropriate management rules can be adopted to ensure the Georgina-Wiso WAP does not lock in negative impacts on environmental and cultural values. Sustainable management of groundwater extraction throughout the CLA should adopt a management approach in line with contemporary best practice, that sets: 1) Volumetric extraction rate limits which in the long-term ensure: A) groundwater flows and levels do not decline in such a way as to compromise the health of the groundwater dependent ecosystems, water quality and aquifer integrity. This requires careful analysis of recharge and discharge flux rates, environmental dependencies on these flows, and the extent of ‘capture’ and drawdown caused by pumping at different rates. B) the renewability of groundwater resources, ensuring prevention of long-term storage depletion and/or detrimental capture of surface flows - recognising the value of the Roper River, Mataranka springs and other GDEs supported by the CLA. 2) Clearly defined and well monitored groundwater level thresholds, determined to be the elevations required to sustain environmental and cultural values of groundwater dependent sites and ecosystems – including through the maintenance of throughflows between the CLA basins. When these levels are approached or crossed, reductions in groundwater pumping should be triggered, in line with level-based management approaches adopted in other parts of Australia and internationally. Trigger levels must be set appropriate distances from environmental assets seeking to be protected to account for time-lags. Setting both a cap on total extractions in declared management zones, along with a series of water level thresholds and buffer zones to protect GDEs, would be in line with international best practices, if implemented alongside a robust monitoring program. Further, any rules developed to allow trading of groundwater should restrict the trade of extraction permits into areas close to high value GDEs. Together, these measures would ensure protection of key values supported by the CLA’s groundwater. This management approach should be informed by a continuing program of inter-disciplinary science and community consultation, focusing on groundwater requirements of GDEs, and modelling to determine relationships between flows to these, extraction volumes, gradients, and time. Knowledge gaps which should be addressed urgently include better qualitative and quantitative information on inter-basin and inter-aquifer flows (topics currently being investigated), better quantification of flows from the CLA and other aquifers to springs and streams (including those that have been less studied than Mataranka Thermal Pools and the Roper River), and eco-hydrological studies (including more extensive stygofauna surveys). These studies should determine the groundwater levels, flow rates and quality required to sustain key environmental and cultural values, as well as possible downstream consequences of reduced spring flows, river baseflows and groundwater throughflows of various magnitudes. Understanding what community stakeholders consider to be acceptable risks and impacts, and making public all relevant supporting scientific data and analysis informing WAP rules, should form part of the process of determining extraction rate caps and triggers. There is also a need to consider climate change and variability, with mechanisms to account for this built into long-term integrated water resources management.